Aligments for a candidate for gcvT in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for gcvT in Shewanella sp. ANA-3

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 7026359 Shewana3_3501 glycine cleavage system aminomethyltransferase T (RefSeq)

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__ANA3:7026359
          Length = 364

 Score =  508 bits (1307), Expect = e-148
 Identities = 246/361 (68%), Positives = 296/361 (81%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           MA +T L+ +H    A+MVDFHGW MPL+YGSQI+EHHAVR DAGMFDVSHMT+VD+ G+
Sbjct: 1   MANKTVLFNKHLESNAKMVDFHGWDMPLNYGSQIEEHHAVRQDAGMFDVSHMTVVDVTGT 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
               FLR LLANDVAKL   GKALY GML+ + G+IDDLI YY T+ F+R+VVNSATREK
Sbjct: 61  DACAFLRKLLANDVAKLKVPGKALYGGMLDDNAGIIDDLITYYLTDTFYRVVVNSATREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+WI + ++ F + +T R +L+MIAVQGPNA+AKAA +F+  Q  A+EGMKPFFG QAG
Sbjct: 121 DLAWIAKQSQGFDVTVTERPELAMIAVQGPNAKAKAAAVFSADQNAAIEGMKPFFGKQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGE GYEI +P  +A   W+AL++ GVKPCGLGARDTLRLEAGMNLYG +M
Sbjct: 181 SLFIATTGYTGEVGYEIIVPETEAEALWQALLDQGVKPCGLGARDTLRLEAGMNLYGLDM 240

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300
           DETI+PLAANMGWTIAWEP DRDFIGR+ALE  R+ GT+KLVGLVM EKGVLR+++PV F
Sbjct: 241 DETINPLAANMGWTIAWEPTDRDFIGRQALEALRDAGTDKLVGLVMEEKGVLRHDMPVFF 300

Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360
           TDA G + +G+ITSGTFSPTLGYSIA+ARVP  IG+TA V++R + + V+V  P FVRNG
Sbjct: 301 TDAAGVEQQGVITSGTFSPTLGYSIAMARVPNSIGDTAEVEMRKKRVAVRVVAPNFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 361


Lambda     K      H
   0.320    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 486
Number of extensions: 12
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 7026359 Shewana3_3501 (glycine cleavage system aminomethyltransferase T (RefSeq))
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00528.hmm
# target sequence database:        /tmp/gapView.31355.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     3e-140  453.2   0.1   3.4e-140  453.0   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7026359  Shewana3_3501 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026359  Shewana3_3501 glycine cleavage system aminomethyltransferase T (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.0   0.1  3.4e-140  3.4e-140       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 453.0 bits;  conditional E-value: 3.4e-140
                         TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk 78 
                                       ++t L++ h e  +k+vdf+Gw +P++y+s+ieeh+avr++aG+fDvshm+ v+++G+++ +fL++llanDv++L +
  lcl|FitnessBrowser__ANA3:7026359   3 NKTVLFNKHLESNAKMVDFHGWDMPLNYGSQIEEHHAVRQDAGMFDVSHMTVVDVTGTDACAFLRKLLANDVAKLKV 79 
                                       79*************************************************************************98 PP

                         TIGR00528  79 .GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....k 150
                                        Gka+y ++l  + G++DDli y+ ++  ++++vvn+at+ekDl+w+ ++ +++    t + e++++a+qGP    k
  lcl|FitnessBrowser__ANA3:7026359  80 pGKALYGGMLDDNAGIIDDLITYYLTDT-FYRVVVNSATREKDLAWIAKQSQGFDVTVTERPELAMIAVQGPnakaK 155
                                       8*************************99.*******************************************99999 PP

                         TIGR00528 151 aktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDt 227
                                       a++++   +++a+eg+k+ff+ q++ l     +ia+tGytGe G+ei+v++ +a  lw++l+++ gvkP+GLgarDt
  lcl|FitnessBrowser__ANA3:7026359 156 AAAVFSADQNAAIEGMKPFFGKQAGSL-----FIATTGYTGEVGYEIIVPETEAEALWQALLDQ-GVKPCGLGARDT 226
                                       999************************.....********************************.************ PP

                         TIGR00528 228 LrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt. 303
                                       Lrleagm+LyG ++de+i Pl+a++gw++++e++++dfiGr++le  ++ gt+k lvGl+m ekg++r++++v++t 
  lcl|FitnessBrowser__ANA3:7026359 227 LRLEAGMNLYGLDMDETINPLAANMGWTIAWEPTDRDFIGRQALEALRDAGTDK-LVGLVMEEKGVLRHDMPVFFTd 302
                                       ****************************************************99.*********************4 PP

                         TIGR00528 304 .ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                         g ++ G++tsGt+sPtLg++ia+a+v+   + iG+++eve+r+k v ++vv + fvr+
  lcl|FitnessBrowser__ANA3:7026359 303 aAGVEQQGVITSGTFSPTLGYSIAMARVP---NSIGDTAEVEMRKKRVAVRVVAPNFVRN 359
                                       446799***********************...99***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (364 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.62
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources